The treatment of colorectal cancer (CRC) might be improved by the identification of a signalling pathway that could be targeted with novel therapeutics. The results of this study indicate that the taurine transporter SLC6A6 is highly expressed in CRC cells compared with normal colonocytes. SLC6A6 knockdown (KD) attenuated cell survival and was accompanied by enhanced drug sensitivity to 5-fluorouracil (5-FU), doxycycline (DOX) and SN-38. Both the population frequency of the side population (SP) cells and their cancer stem cell (CSC)-like properties (such as tumour initiation, differentiation and chemoresistance) were abrogated by SLC6A6-KD. Conversely, SLC6A6 overexpression increased cell survival and the proportion of SP cells, enhancing multidrug resistance (MDR). Additionally, SLC6A6-siRNA treatment enhanced the cytotoxic effects of all 3 drugs, whereas the efficacy of ABCG2-siRNA treatment was limited to its 2 substrate drugs, DOX and SN-38. This study indicates that SLC6A6 plays an important role in the maintenance of CSC characteristics, thus promoting cell survival signalling and chemoresistance. Therefore, SLC6A6 inhibition may be a promising therapeutic strategy for refractory CRC.